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  "Package": "idr2d",
  "Title": "Irreproducible Discovery Rate for Genomic Interactions Data",
  "Version": "1.26.0",
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  "Description": "A tool to measure reproducibility between genomic\nexperiments that produce two-dimensional peaks (interactions\nbetween peaks), such as ChIA-PET, HiChIP, and HiC. idr2d is an\nextension of the original idr package, which is intended for\n(one-dimensional) ChIP-seq peaks.",
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  "URL": "https://idr2d.mit.edu",
  "VignetteBuilder": "knitr",
  "biocViews": "DNA3DStructure, GeneRegulation, PeakDetection, Epigenetics,\nFunctionalGenomics, Classification, HiC",
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  "Date/Publication": "2026-04-28 12:50:53 UTC",
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    "hic"
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    "determine_anchor_overlap",
    "draw_hic_contact_map",
    "draw_idr_distribution_histogram",
    "draw_rank_idr_scatterplot",
    "draw_value_idr_scatterplot",
    "establish_bijection",
    "establish_bijection1d",
    "establish_bijection2d",
    "establish_overlap1d",
    "establish_overlap2d",
    "estimate_idr",
    "estimate_idr1d",
    "estimate_idr2d",
    "estimate_idr2d_hic",
    "parse_hic_pro_matrix",
    "parse_juicer_matrix",
    "preprocess",
    "remove_nonstandard_chromosomes1d",
    "remove_nonstandard_chromosomes2d"
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      "name": "chiapet",
      "title": "Example Genomic Interaction Data Set",
      "object": "chiapet",
      "file": "chiapet.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "chipseq",
      "title": "Example Genomic Peak Data Set",
      "object": "chipseq",
      "file": "chipseq.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "hic",
      "title": "Example Hi-C data set",
      "object": "hic",
      "file": "hic.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
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  "_help": [
    {
      "page": "calculate_midpoint_distance1d",
      "title": "Distance between Midpoints of two Peaks",
      "topics": [
        "calculate_midpoint_distance1d"
      ]
    },
    {
      "page": "calculate_midpoint_distance2d",
      "title": "Distance between Anchor Midpoints of two Interactions",
      "topics": [
        "calculate_midpoint_distance2d"
      ]
    },
    {
      "page": "calculate_relative_overlap1d",
      "title": "Relative Anchor Overlap of two Peaks",
      "topics": [
        "calculate_relative_overlap1d"
      ]
    },
    {
      "page": "calculate_relative_overlap2d",
      "title": "Relative Anchor Overlap of two Interactions",
      "topics": [
        "calculate_relative_overlap2d"
      ]
    },
    {
      "page": "chiapet",
      "title": "Example Genomic Interaction Data Set",
      "topics": [
        "chiapet"
      ]
    },
    {
      "page": "chipseq",
      "title": "Example Genomic Peak Data Set",
      "topics": [
        "chipseq"
      ]
    },
    {
      "page": "determine_anchor_overlap",
      "title": "Identifies Overlapping Anchors",
      "topics": [
        "determine_anchor_overlap"
      ]
    },
    {
      "page": "draw_hic_contact_map",
      "title": "Create Hi-C contact map",
      "topics": [
        "draw_hic_contact_map"
      ]
    },
    {
      "page": "draw_idr_distribution_histogram",
      "title": "Create histogram of IDR values",
      "topics": [
        "draw_idr_distribution_histogram"
      ]
    },
    {
      "page": "draw_rank_idr_scatterplot",
      "title": "Create scatterplot of IDR values",
      "topics": [
        "draw_rank_idr_scatterplot"
      ]
    },
    {
      "page": "draw_value_idr_scatterplot",
      "title": "Create scatterplot of IDR values",
      "topics": [
        "draw_value_idr_scatterplot"
      ]
    },
    {
      "page": "establish_bijection",
      "title": "Finds One-to-One Correspondence between Peaks or interactions from Replicate 1 and 2",
      "topics": [
        "establish_bijection"
      ]
    },
    {
      "page": "establish_bijection1d",
      "title": "Finds One-to-One Correspondence between Peaks from Replicate 1 and 2",
      "topics": [
        "establish_bijection1d"
      ]
    },
    {
      "page": "establish_bijection2d",
      "title": "Finds One-to-One Correspondence between Interactions from Replicate 1 and 2",
      "topics": [
        "establish_bijection2d"
      ]
    },
    {
      "page": "establish_overlap1d",
      "title": "Establish m:n Mapping Between Peaks from Replicate 1 and 2",
      "topics": [
        "establish_overlap1d"
      ]
    },
    {
      "page": "establish_overlap2d",
      "title": "Establish m:n mapping between interactions from replicate 1 and 2",
      "topics": [
        "establish_overlap2d"
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    },
    {
      "page": "estimate_idr",
      "title": "Estimates IDR for Genomic Peaks or Genomic Interactions",
      "topics": [
        "estimate_idr"
      ]
    },
    {
      "page": "estimate_idr1d",
      "title": "Estimates IDR for Genomic Peak Data",
      "topics": [
        "estimate_idr1d"
      ]
    },
    {
      "page": "estimate_idr2d",
      "title": "Estimates IDR for Genomic Interaction Data",
      "topics": [
        "estimate_idr2d"
      ]
    },
    {
      "page": "estimate_idr2d_hic",
      "title": "Estimates IDR for Genomic Interactions measured by Hi-C experiments",
      "topics": [
        "estimate_idr2d_hic"
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      "title": "Example Hi-C data set",
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      "title": "Parse .matrix and .bed files from HiC-Pro for IDR2D analysis",
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      "title": "Parse .hic files from Juicer for IDR2D analysis",
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    },
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